Err .. how do I explain this ...
HDMI -> Designed for Streaming HiDef Video/Audio between a single source and single destination device, predominantly in a single direction, including copyright signaling/flags.
USB3 -> Overclocked version of Overclocked version of system designed to transfer small amounts of information between many devices - particularly bad at streaming large amounts of data, great at addressing/transferring data to/from many devices simultaneously, either direction.
And just to complete the love triangle:
SATA (1.5Gbps/3Gbps/6Gbps) -> Designed for high speed data transfer of small or large amounts of data between single source and single destination device, either direction.
No single interface is particularly useful in all cases ....
On the Data front, it's USB3 & Sata throwing punches, but USB3 just won't have the low latency required for an internal device.
On the video front, it's Sata & HDMI duking it out, but HDMI has a more robust connector, for when stone masons come home and decide that their home theatre system needs to be reconfigured with a mallet
USB3 will win the day, thanks to it's backwards compatibility & established code base